(A) Close-up view of the U-UU bulge in DenvBS, drawn from the lowest energy structure (left) and superposition of 10 representative NMR structures (right). Ura12 and Ura30 are coplanar, potentially forming an unstable base pair (no NH peak is visible in 2D spectra), while Ura29 stacks between Gua28 and Ura30, retaining continuous stacking. (B) A close-up view of the internal loop in DenvTSL, taken from the lowest energy structure (left) and the superposition of 10 representative NMR structures (right). Nucleotides Cyt7–Ade9 and Gua20–Ade22 across the internal loop stack within the helix. Although no evidence of noncanonical base-pair formation in this region was observed in NMR spectra, uninterrupted sequential NOEs were observed (Supplemental Fig. S5). (C) A close-up view of the terminal loop in DenvTSL from the lowest energy structure (left) and the superposition of 10 representative NMR structures (right). In this last image, nucleotides are colored differently for clarity (C13 in green, A14 in cyan, G15 in magenta, and U16 in yellow). In all 10 structures, Gua15 points toward the major groove while Ade14 and Ura16 point outward toward the solvent, and Cyt13 is poorly defined.
